Fig. 4

Influence of pathway length and interaction type on P53 DBD communication. a 2D topology diagram (on the left) and 3D structure (on the right) of p53 DBD. The diagram was taken from PDBsum [71] and the colours were modified to put in evidence the S-type immunoglobulin-like fold of p53 DBD: the first β-sheet is in pink, the second β-sheet is in red. The 3D structure (average MD conformation) is represented as a cartoon, where the 11 β-strands of the protein are coloured in grey tones and labelled. The clique-based communication blocks identified by COMMA are colored in blue tones. b–g Pathway-based communication blocks identified by COMMA by using information from all non-covalent interactions (b–d) or only interactions involving side chains (e–g), and by considering only pathways longer than 3 (b, e), 5 (c, f) or 7 (d, g) residues. The communication blocks are represented as subgraphs in the PCN (on the left) and are mapped on the average MD conformation (on the right). The edges on the subgraphs and the residues on the 3D structure are coloured according to the communication blocks they belong to. The nodes in the subgraphs are coloured in grey tones, indicating the β-strand they belong to